Question

How can I Push my apk from the Data Folder to the System/App Folder using a Rooted Device, programmatically using Runtime.getRuntime().exe.

Should I use Pull, Push or Cat Command and how?

Does it will affect Shared Prefs or anything?

Answer 1

Try

Runtime.getRuntime().exec("pm install -r "/path/to/yourfilename.apk";)

Usage
pm install [-l] [-r] [-t] [-i INSTALLER_PACKAGE_NAME] [-s] [-f]
[–algo –key –iv ] PATH

options :

-l: install the package with FORWARD_LOCK.
-r: reinstall an exisiting app, keeping its data.
-t: allow test .apks to be installed.
-i: specify the installer package name.
-s: install package on sdcard.
-f: install package on internal flash.

Depending on your usage of the -r parameter, it will affect the shared preferences xml files (use to not lose).